sylvinite/arteria-packs

StackStorm packs to automate sequencing center operations

arteria-packs

NOTE: This is very much a work in progress, mostly containing dummy workflows so far.

StackStorm pack to setup automation workflow taking data from the sequencer to delivery on the remote host...

If you are using the arteria-provisioning this directory should be mounted under the /opt/stackstorm/packs/arteria-packs (make sure to set the path in the Vagrant file). To load all actions, rules, etc, run st2 run packs.load register=all.

Getting an authentication token

Get your auth token setup (substitute for correct user and password as necessary) :

export ST2_AUTH_TOKEN=$(st2 auth --only-token testu -p testp)

Example of starting a workflow

Now you should be good to go. Here's an example of how to run a action:

 st2 run arteria-packs.ngi_uu_workflow runfolder=/data/testarteria1/150605_M00485_0183_000000000-ABGT6_testbio14 host=testarteria1

To see the result of a run - you can first list the executions:

st2 execution list

Pick the one you're interested in and:

st2 execution get --detail --json <your execution id>

Examples of using traces to track a runfolder

Each execution will get it's own unique id when run by StackStorm. However it can be convenient to be able to tag executions in other ways. Such as being able to see all executions for a particular runfolder for example. You can achieve this by using the --trace-tag argument when staring a job, e.g:

st2 run arteria-packs.ngi_uu_workflow \
    runfolder=/data/testarteria1/150605_M00485_0183_000000000-ABGT6_testbio14 \
    host=testarteria1 \
    --trace-tag 150605_M00485_0183_000000000-ABGT6_testbio14

Now you can search for the trace-tag using:

st2 trace list --trace-tag 150605_M00485_0183_000000000-ABGT6_testbio14

To find more information about a particular trace, use:

st2 trace get <trace id>

From there you can go to getting more information on the executions using:

st2 execution get <execution id>

This will list all executions and triggers associated with the tag.

All of this has been wrapped by scripts/trace_runfolder.py, which allows you to get all excutions of a workflow associated with a tag, e.g.:

python scripts/trace_runfolder.py --tag 150605_M00485_0183_000000000-ABGT6_testbio14 | xargs -n1 st2 execution get

For automatic triggering the trace tag can be injected via the sensor. For more info on traces, see: http://docs.stackstorm.com/traces.html